# ##################################################################################################
#  Disclaimer                                                                                      #
#  This file is a python3 translation of AutoDockTools (v.1.5.7)                                   #
#  Modifications made by Valdes-Tresanco MS (https://github.com/Valdes-Tresanco-MS)                #
#  Tested by Valdes-Tresanco-MS and Valdes-Tresanco ME                                             #
#  There is no guarantee that it works like the original distribution,                             #
#  but feel free to tell us if you get any difference to correct the code.                         #
#                                                                                                  #
#  Please use this cite the original reference.                                                    #
#  If you think my work helps you, just keep this note intact on your program.                     #
#                                                                                                  #
#  Modification date: 4/7/20 5:48                                                                  #
#                                                                                                  #
# ##################################################################################################

###################################################################
#  Kollman united atom (polar-Hydrogen) charges.
#
#  Garrett M. Morris, July 6, 1992. Original version in "awk".
#  Revised:        September 18, 1992,
#  Revised:        March 25, 1993.
#  Pythonised: Sometime in the 21st Century.
#
#
#  Now recognizes the alternate location indicator and 
#  chain-identifier correctly.
#

#
#  VERSION 3.0
#

#  Create a dictionary of partial atomic charges based on the 
#  Kollman United Atom Charge Set (KOLLUA), whose keys
#  are a tuple of the residue name and atom name:
#######################################################################

# $Header: /opt/cvs/python/packages/share1.5/MolKit/data/qkollua.py,v 1.1 2003/11/11 23:57:19 rhuey Exp $
#
# $Id: qkollua.py,v 1.1 2003/11/11 23:57:19 rhuey Exp $
#

q = {}

#
# ALA 6 0.000 Alanine, polypeptide residue
#
q["ALA"] = {}
q["ALA"]["N"] = -0.5200
q["ALA"]["CA"] = 0.2150
q["ALA"]["HN"] = 0.2480
q["ALA"]["C"] = 0.5260
q["ALA"]["O"] = -0.5000
q["ALA"]["CB"] = 0.0310
#
# ARG 17 -12.480 Arginine(positive side chain), polypeptide residue
#
q["ARG"] = {}
q["ARG"]["N"] = -0.5200
q["ARG"]["CA"] = 0.2370
q["ARG"]["HN"] = 0.2480
q["ARG"]["C"] = 0.5260
q["ARG"]["O"] = -0.5000
q["ARG"]["CB"] = 0.0490
q["ARG"]["CG"] = 0.0580
q["ARG"]["CD"] = 0.1110
q["ARG"]["NE"] = -0.4930
# adjusted charge on CZ by +.001
q["ARG"]["CZ"] = 0.8140
q["ARG"]["NH1"] = -0.6340
q["ARG"]["NH2"] = -0.6340
q["ARG"]["HE"] = 0.2940
q["ARG"]["HH11"] = 0.3610
q["ARG"]["HH12"] = 0.3610
q["ARG"]["HH21"] = 0.3610
q["ARG"]["HH22"] = 0.3610
#
# ASN 11 0.000 Asparagine, polypeptide residue
#
q["ASN"] = {}
q["ASN"]["N"] = -0.5200
q["ASN"]["CA"] = 0.2170
q["ASN"]["HN"] = 0.2480
q["ASN"]["C"] = 0.5260
q["ASN"]["O"] = -0.5000
q["ASN"]["CB"] = 0.0030
q["ASN"]["CG"] = 0.6750
q["ASN"]["OD1"] = -0.4700
q["ASN"]["ND2"] = -0.8670
q["ASN"]["HD21"] = 0.3440
q["ASN"]["HD22"] = 0.3440
#
# ASPN 11 0.000 Aspartate(negative side chain), positive N-terminus
#
q["ASPN"] = {}
q["ASPN"]["N"] = -0.2630
q["ASPN"]["CA"] = 0.3010
q["ASPN"]["C"] = 0.5260
q["ASPN"]["O"] = -0.5000
q["ASPN"]["CB"] = -0.2080
q["ASPN"]["CG"] = 0.6200
q["ASPN"]["OD1"] = -0.7060
q["ASPN"]["OD2"] = -0.7060
#
# ASP 9 3.650 Aspartate(negative side chain), polypeptide residue
#
q["ASP"] = {}
q["ASP"]["N"] = -0.5200
q["ASP"]["CA"] = 0.2460
q["ASP"]["HN"] = 0.2480
q["ASP"]["C"] = 0.5260
q["ASP"]["O"] = -0.5000
q["ASP"]["CB"] = -0.2080
q["ASP"]["CG"] = 0.6200
q["ASP"]["OD1"] = -0.7060
q["ASP"]["OD2"] = -0.7060
#
# CYS 7 0.000 Cystine(sulfide bridge), polypeptide residue
#
q["CYS"] = {}
q["CYS"]["N"] = -0.5200
q["CYS"]["CA"] = 0.0880
q["CYS"]["HN"] = 0.2480
q["CYS"]["C"] = 0.5260
q["CYS"]["O"] = -0.5000
q["CYS"]["CB"] = 0.1430
q["CYS"]["SG"] = 0.0150
#
# CYSH 8 0.000 Cysteine, polypeptide residue
#
q["CYSH"] = {}
q["CYSH"]["N"] = -0.5200
q["CYSH"]["CA"] = 0.1460
q["CYSH"]["HN"] = 0.2480
q["CYSH"]["C"] = 0.5260
q["CYSH"]["O"] = -0.5000
q["CYSH"]["CB"] = 0.1000
q["CYSH"]["SG"] = -0.1350
q["CYSH"]["HG"] = 0.1350
#
# CYHC 9 0.000 Cysteine, negative C-terminus
#
q["CYHC"] = {}
q["CYHC"]["N"] = -0.5200
q["CYHC"]["CA"] = 0.1400
q["CYHC"]["HN"] = 0.2480
q["CYHC"]["C"] = 0.4440
q["CYHC"]["O"] = -0.7060
q["CYHC"]["CB"] = 0.1000
q["CYHC"]["SG"] = -0.1350
q["CYHC"]["HG"] = 0.1350
#
# GLU 10 4.250 Glutamate(negative side chain), polypeptide residue
#
q["GLU"] = {}
q["GLU"]["N"] = -0.5200
q["GLU"]["CA"] = 0.2460
q["GLU"]["HN"] = 0.2480
q["GLU"]["C"] = 0.5260
q["GLU"]["O"] = -0.5000
q["GLU"]["CB"] = -0.0000
q["GLU"]["CG"] = -0.2080
q["GLU"]["CD"] = 0.6200
q["GLU"]["OE1"] = -0.7060
q["GLU"]["OE2"] = -0.7060
#
# GLN 12 0.000 Glutamine, polypeptide residue
#
q["GLN"] = {}
q["GLN"]["N"] = -0.5200
q["GLN"]["CA"] = 0.2100
q["GLN"]["HN"] = 0.2480
q["GLN"]["C"] = 0.5260
q["GLN"]["O"] = -0.5000
q["GLN"]["CB"] = 0.0530
q["GLN"]["CG"] = -0.0430
q["GLN"]["CD"] = 0.6750
q["GLN"]["OE1"] = -0.4700
q["GLN"]["NE2"] = -0.8670
q["GLN"]["HE21"] = 0.3440
q["GLN"]["HE22"] = 0.3440
#
# GLY 5 0.000 Glycine, polypeptide residue
#
q["GLY"] = {}
q["GLY"]["N"] = -0.5200
q["GLY"]["CA"] = 0.2460
q["GLY"]["HN"] = 0.2480
q["GLY"]["C"] = 0.5260
q["GLY"]["O"] = -0.5000
#
# HIS 12 6.000 Histidine(H on NE),polypeptide residue
#
q["HIS"] = {}
q["HIS"]["N"] = -0.5200
q["HIS"]["CA"] = 0.2190
q["HIS"]["HN"] = 0.2480
q["HIS"]["C"] = 0.5260
q["HIS"]["O"] = -0.5000
q["HIS"]["CB"] = 0.0600
q["HIS"]["CG"] = 0.1120
q["HIS"]["ND1"] = -0.5270
q["HIS"]["CE1"] = 0.3840
q["HIS"]["NE2"] = -0.4440
q["HIS"]["CD2"] = 0.1220
q["HIS"]["HE2"] = 0.3200
# other name variants: amber, lpdb
q["HIE"] = q["HSE"] = q["HIS"]
#
# HIS+ 13 -6.000 Histidine(positive side chain), polypeptide residue
#
q["HIS+"] = {}
q["HIS+"]["N"] = -0.5200
q["HIS+"]["CA"] = 0.1950
q["HIS+"]["HN"] = 0.2480
q["HIS+"]["C"] = 0.5260
q["HIS+"]["O"] = -0.5000
q["HIS+"]["CB"] = 0.2110
q["HIS+"]["CG"] = 0.1030
q["HIS+"]["ND1"] = -0.6130
q["HIS+"]["CE1"] = 0.7190
q["HIS+"]["NE2"] = -0.6860
q["HIS+"]["CD2"] = 0.3530
q["HIS+"]["HD1"] = 0.4780
q["HIS+"]["HE2"] = 0.4860
# other name variants: amber, lpdb
q["HIP"] = q["HSP"] = q["HIS+"]
#
# HISD 12 6.000 Histidine(H on ND),polypeptide residue
#
q["HISD"] = {}
q["HISD"]["N"] = -0.5200
q["HISD"]["CA"] = 0.2190
q["HISD"]["HN"] = 0.2480
q["HISD"]["C"] = 0.5260
q["HISD"]["O"] = -0.5000
q["HISD"]["CB"] = 0.0600
q["HISD"]["CG"] = 0.0890
q["HISD"]["ND1"] = -0.4440
q["HISD"]["CE1"] = 0.3840
q["HISD"]["NE2"] = -0.5270
q["HISD"]["CD2"] = 0.1450
q["HISD"]["HD1"] = 0.3200
# other name variants: amber, lpdb
q["HID"] = q["HSD"] = q["HISD"]
#
# ILE 9 0.000 Isoleucine, polypeptide residue
#
q["ILE"] = {}
q["ILE"]["N"] = -0.5200
q["ILE"]["CA"] = 0.1990
q["ILE"]["HN"] = 0.2480
q["ILE"]["C"] = 0.5260
q["ILE"]["O"] = -0.5000
q["ILE"]["CB"] = 0.0300
q["ILE"]["CG2"] = 0.0010
q["ILE"]["CG1"] = 0.0170
q["ILE"]["CD1"] = -0.0010
#
# ILEC 10 0.000 Isoleucine, negative C-terminus
#
q["ILEC"] = {}
q["ILEC"]["N"] = -0.5200
q["ILEC"]["CA"] = 0.1930
q["ILEC"]["HN"] = 0.2480
q["ILEC"]["C"] = 0.4440
q["ILEC"]["O"] = -0.7060
q["ILEC"]["CB"] = 0.0300
q["ILEC"]["CG2"] = 0.0010
q["ILEC"]["CG1"] = 0.0170
q["ILEC"]["CD1"] = -0.0010
#
# LEU 9 0.000 Leucine, polypeptide residue
#
q["LEU"] = {}
q["LEU"]["N"] = -0.5200
q["LEU"]["CA"] = 0.2040
q["LEU"]["HN"] = 0.2480
q["LEU"]["C"] = 0.5260
q["LEU"]["O"] = -0.5000
q["LEU"]["CB"] = 0.0160
q["LEU"]["CG"] = 0.0540
q["LEU"]["CD1"] = -0.0140
q["LEU"]["CD2"] = -0.0140
#
# LEUC 10 0.000 Leucine, negative C-terminus
#
q["LEUC"] = {}
q["LEUC"]["N"] = -0.5200
q["LEUC"]["CA"] = 0.1980
q["LEUC"]["HN"] = 0.2480
q["LEUC"]["C"] = 0.4440
q["LEUC"]["O"] = -0.7060
q["LEUC"]["CB"] = 0.0160
q["LEUC"]["CG"] = 0.0540
q["LEUC"]["CD1"] = -0.0140
q["LEUC"]["CD2"] = -0.0140
#
# LYS 13 -10.530 Lysine(positive side chain), polypeptide residue
#
q["LYS"] = {}
q["LYS"]["N"] = -0.5200
q["LYS"]["CA"] = 0.2270
q["LYS"]["HN"] = 0.2480
q["LYS"]["C"] = 0.5260
q["LYS"]["O"] = -0.5000
q["LYS"]["CB"] = 0.0390
q["LYS"]["CG"] = 0.0530
q["LYS"]["CD"] = 0.0480
q["LYS"]["CE"] = 0.2180
q["LYS"]["NZ"] = -0.2720
q["LYS"]["HZ1"] = 0.3110
q["LYS"]["HZ2"] = 0.3110
q["LYS"]["HZ3"] = 0.3110
#
# LYSN 15 0.000 Lysine(positive side chain), positive N-terminus
#
q["LYSN"] = {}
q["LYSN"]["N"] = -0.2630
q["LYSN"]["CA"] = 0.2820
q["LYSN"]["C"] = 0.5260
q["LYSN"]["O"] = -0.5000
q["LYSN"]["CB"] = 0.0390
q["LYSN"]["CG"] = 0.0530
q["LYSN"]["CD"] = 0.0480
q["LYSN"]["CE"] = 0.2180
q["LYSN"]["NZ"] = -0.2720
q["LYSN"]["HZ1"] = 0.3110
q["LYSN"]["HZ2"] = 0.3110
q["LYSN"]["HZ3"] = 0.3110
#
# MET 9 0.000 Methionine, polypeptide residue
#
q["MET"] = {}
q["MET"]["N"] = -0.5200
q["MET"]["CA"] = 0.1370
q["MET"]["HN"] = 0.2480
q["MET"]["C"] = 0.5260
q["MET"]["O"] = -0.5000
q["MET"]["CB"] = 0.0370
q["MET"]["CG"] = 0.0900
q["MET"]["SD"] = -0.0250
q["MET"]["CE"] = 0.0070
#
# PCA 9 0.000 cyclized gln, polypeptide residue
#
q["PCA"] = {}
q["PCA"]["N"] = -0.5200
q["PCA"]["CA"] = 0.2100
q["PCA"]["CB"] = 0.0530
q["PCA"]["CG"] = -0.0430
q["PCA"]["CD"] = 0.5260
q["PCA"]["OE"] = -0.5000
q["PCA"]["HN"] = 0.2480
q["PCA"]["C"] = 0.5260
q["PCA"]["O"] = -0.5000
#
# PHE 12 0.000 Phenylalanine, polypeptide residue
#
q["PHE"] = {}
q["PHE"]["N"] = -0.5200
q["PHE"]["CA"] = 0.2140
q["PHE"]["HN"] = 0.2480
q["PHE"]["C"] = 0.5260
q["PHE"]["O"] = -0.5000
q["PHE"]["CB"] = 0.0380
q["PHE"]["CG"] = 0.0110
q["PHE"]["CD1"] = -0.0110
q["PHE"]["CE1"] = 0.0040
q["PHE"]["CZ"] = -0.0030
q["PHE"]["CE2"] = 0.0040
q["PHE"]["CD2"] = -0.0110
#
# PRO 7 0.000 Proline, polypeptide residue
#
q["PRO"] = {}
q["PRO"]["N"] = -0.2570
q["PRO"]["CA"] = 0.1120
q["PRO"]["CD"] = 0.0840
q["PRO"]["C"] = 0.5260
q["PRO"]["O"] = -0.5000
q["PRO"]["CB"] = -0.0010
q["PRO"]["CG"] = 0.0360
#
# SER 8 0.000 Serine, polypeptide residue
#
q["SER"] = {}
q["SER"]["N"] = -0.5200
q["SER"]["CA"] = 0.2920
q["SER"]["HN"] = 0.2480
q["SER"]["C"] = 0.5260
q["SER"]["O"] = -0.5000
q["SER"]["CB"] = 0.1940
q["SER"]["OG"] = -0.5500
q["SER"]["HG"] = 0.3100
#
# THR 9 0.000 Threonine, polypeptide residue
#
q["THR"] = {}
q["THR"]["N"] = -0.5200
q["THR"]["CA"] = 0.2680
q["THR"]["HN"] = 0.2480
q["THR"]["C"] = 0.5260
q["THR"]["O"] = -0.5000
q["THR"]["CB"] = 0.2110
q["THR"]["OG1"] = -0.5500
q["THR"]["HG1"] = 0.3100
q["THR"]["CG2"] = 0.0070
#
# TRP 16 0.000 Tryptophan, polypeptide residue
#
q["TRP"] = {}
q["TRP"]["N"] = -0.5200
q["TRP"]["CA"] = 0.2480
q["TRP"]["HN"] = 0.2480
q["TRP"]["C"] = 0.5260
q["TRP"]["O"] = -0.5000
q["TRP"]["CB"] = 0.0200
q["TRP"]["CG"] = 0.0460
q["TRP"]["CD1"] = 0.1170
q["TRP"]["NE1"] = -0.3300
q["TRP"]["CE2"] = 0.0000
q["TRP"]["CD2"] = -0.2750
q["TRP"]["HE1"] = 0.2940
q["TRP"]["CE3"] = 0.1450
q["TRP"]["CZ3"] = -0.0820
q["TRP"]["CH2"] = 0.0340
q["TRP"]["CZ2"] = 0.0290
#
# TYR 14 -10.070 Tyrosine, polypeptide residue
#
q["TYR"] = {}
q["TYR"]["N"] = -0.5200
q["TYR"]["CA"] = 0.2450
q["TYR"]["HN"] = 0.2480
q["TYR"]["C"] = 0.5260
q["TYR"]["O"] = -0.5000
q["TYR"]["CB"] = 0.0220
q["TYR"]["CG"] = -0.0010
q["TYR"]["CD1"] = -0.0350
q["TYR"]["CE1"] = 0.1000
q["TYR"]["CZ"] = -0.1210
q["TYR"]["OH"] = -0.3680
q["TYR"]["HH"] = 0.3390
q["TYR"]["CE2"] = 0.1000
q["TYR"]["CD2"] = -0.0350
#
# VAL 8 0.000 Valine, polypeptide residue
#
q["VAL"] = {}
q["VAL"]["N"] = -0.5200
q["VAL"]["CA"] = 0.2010
q["VAL"]["HN"] = 0.2480
q["VAL"]["C"] = 0.5260
q["VAL"]["O"] = -0.5000
q["VAL"]["CB"] = 0.0330
q["VAL"]["CG1"] = 0.0060
q["VAL"]["CG2"] = 0.0060
#
# ACE 3 0.000 Acetyl, on N-terminus
#
q["ACE"] = {}
q["ACE"]["CA"] = -0.0260
q["ACE"]["C"] = 0.5260
q["ACE"]["O"] = -0.5000
#
# N-M 3 0.000 N-Methyl, on C-terminus
#
q["N-M"] = {}
q["N-M"]["N"] = -0.5000
q["N-M"]["CA"] = 0.2200
q["N-M"]["HN"] = 0.2800
#
# NH2 3 0.000 NH2, on C-terminus
#
q["NH2"] = {}
q["NH2"]["N"] = -0.5000
q["NH2"]["HN1"] = 0.2500
q["NH2"]["HN2"] = 0.2500
#
# WTR 3 0.000 Water
#
q["WTR"] = {}
q["WTR"]["O"] = -0.8200
q["WTR"]["H1"] = 0.4100
q["WTR"]["H2"] = 0.4100
q["WTR"]["HO"] = 0.4100
q["WTR"]["HO1"] = 0.4100
q["WTR"]["HO2"] = 0.4100
q["WTR"]["O1"] = -0.8200
q["WTR"]["H11"] = 0.4100
q["WTR"]["H12"] = 0.4100
#
# WTX 3 0.000 Water
#
q["WTX"] = {}
q["WTX"]["O"] = -0.8200
q["WTX"]["H1"] = 0.4100
q["WTX"]["H2"] = 0.4100
q["WTX"]["HO"] = 0.4100
q["WTX"]["HO1"] = 0.4100
q["WTX"]["HO2"] = 0.4100
q["WTX"]["O1"] = -0.8200
q["WTX"]["H11"] = 0.4100
q["WTX"]["H12"] = 0.4100
#
# HOH 3 0.000 Water (RCSB Convention)
#
q["HOH"] = {}
q["HOH"]["O"] = -0.8200
q["HOH"]["H1"] = 0.4100
q["HOH"]["H2"] = 0.4100
q["HOH"]["HO"] = 0.4100
q["HOH"]["HO1"] = 0.4100
q["HOH"]["HO2"] = 0.4100
q["HOH"]["O1"] = -0.8200
q["HOH"]["H11"] = 0.4100
q["HOH"]["H12"] = 0.4100
#
# WAT 3 0.000 Water (RCSB Convention)
#
q["WAT"] = {}
q["WAT"]["O"] = -0.8200
q["WAT"]["H1"] = 0.4100
q["WAT"]["H2"] = 0.4100
q["WAT"]["HO"] = 0.4100
q["WAT"]["HO1"] = 0.4100
q["WAT"]["HO2"] = 0.4100
q["WAT"]["O1"] = -0.8200
q["WAT"]["H11"] = 0.4100
q["WAT"]["H12"] = 0.4100
#
# elib
#
#
# the following charges are from uni.in, part of the amber data set
# NB: it names the oxygen in the sugar ring 'O1*' whereas sol_par names it 'O4*'
#  D-ADENOSINE
q["DADE"] = q["  A"] = {}
q["DADE"]["O5*"] = -0.53500
q["DADE"]["O5'"] = -0.53500
q["DADE"]["C5*"] = 0.15300
q["DADE"]["C5'"] = 0.15300
q["DADE"]["C4*"] = 0.18500
q["DADE"]["C4'"] = 0.18500
q["DADE"]["O1*"] = -0.38600
q["DADE"]["O1'"] = -0.38600
q["DADE"]["O4*"] = -0.38600
q["DADE"]["O4'"] = -0.38600
q["DADE"]["C1*"] = 0.50000
q["DADE"]["C1'"] = 0.50000
q["DADE"]["N9"] = -0.45700
q["DADE"]["C8"] = 0.48800
q["DADE"]["N7"] = -0.59900
q["DADE"]["C5"] = -0.15100
q["DADE"]["C6"] = 0.81300
q["DADE"]["N6"] = -0.79300
q["DADE"]["H61"] = 0.33500
q["DADE"]["H62"] = 0.33900
q["DADE"]["N1"] = -0.76000
q["DADE"]["C2"] = 0.57100
q["DADE"]["N3"] = -0.71700
q["DADE"]["C4"] = 0.69500
q["DADE"]["C3*"] = 0.17200
q["DADE"]["C3'"] = 0.17200
q["DADE"]["C2*"] = -0.04700
q["DADE"]["C2'"] = -0.04700
q["DADE"]["O3*"] = -0.53500
q["DADE"]["O3'"] = -0.53500
q["DADE"]["P"] = 1.42900
q["DADE"]["O1P"] = -0.8500
q["DADE"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["DADE"]["H1P"] = 0.00
q["DADE"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["DADE"]["H5*"] = 0.00
q["DADE"]["H5'"] = 0.00
q["DADE"]["H5*1"] = 0.00
q["DADE"]["H5'1"] = 0.00
q["DADE"]["H5*2"] = 0.00
q["DADE"]["H5'2"] = 0.00
q["DADE"]["H4*"] = 0.00
q["DADE"]["H4'"] = 0.00
q["DADE"]["H3*"] = 0.00
q["DADE"]["H3'"] = 0.00
q["DADE"]["H2*1"] = 0.00
q["DADE"]["H2'1"] = 0.00
q["DADE"]["H2*2"] = 0.00
q["DADE"]["H2'2"] = 0.00
q["DADE"]["H1*"] = 0.00
q["DADE"]["H1'"] = 0.00
q["DADE"]["H8"] = 0.00
q["DADE"]["H7"] = 0.00
q["DADE"]["H3"] = 0.00
q["DADE"]["H2"] = 0.00
q["DADE"]["H1"] = 0.00

#  R-ADENOSINE
q["RADE"] = q[" RA"] = {}
q["RADE"]["O5*"] = -0.53500
q["RADE"]["O5'"] = -0.53500
q["RADE"]["C5*"] = 0.17500
q["RADE"]["C5'"] = 0.17500
q["RADE"]["C4*"] = 0.19700
q["RADE"]["C4'"] = 0.19700
q["RADE"]["O1*"] = -0.41300
q["RADE"]["O1'"] = -0.41300
q["RADE"]["O4*"] = -0.41300
q["RADE"]["O4'"] = -0.41300
q["RADE"]["C1*"] = 0.52200
q["RADE"]["C1'"] = 0.52200
q["RADE"]["N9"] = -0.45700
q["RADE"]["C8"] = 0.48800
q["RADE"]["N7"] = -0.59900
q["RADE"]["C5"] = -0.15100
q["RADE"]["C6"] = 0.81300
q["RADE"]["N6"] = -0.79300
q["RADE"]["H61"] = 0.33500
q["RADE"]["H62"] = 0.33900
q["RADE"]["N1"] = -0.76000
q["RADE"]["C2"] = 0.57100
q["RADE"]["N3"] = -0.71700
q["RADE"]["C4"] = 0.69500
q["RADE"]["C3*"] = 0.21000
q["RADE"]["C3'"] = 0.21000
q["RADE"]["C2*"] = 0.08200
q["RADE"]["C2'"] = 0.08200
q["RADE"]["O2*"] = -0.51200  # for rna only
q["RADE"]["O2'"] = -0.51200  # for rna only
q["RADE"]["HO2*"] = 0.31600  # for rna only
q["RADE"]["HO2'"] = 0.31600  # for rna only
q["RADE"]["O3*"] = -0.53500
q["RADE"]["O3'"] = -0.53500
q["RADE"]["P"] = 1.42900
q["RADE"]["O1P"] = -0.8500
q["RADE"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["RADE"]["H1P"] = 0.00
q["RADE"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["RADE"]["H5*"] = 0.00
q["RADE"]["H5'"] = 0.00
q["RADE"]["H5*1"] = 0.00
q["RADE"]["H5'1"] = 0.00
q["RADE"]["H5*2"] = 0.00
q["RADE"]["H5'2"] = 0.00
q["RADE"]["H4*"] = 0.00
q["RADE"]["H4'"] = 0.00
q["RADE"]["H3*"] = 0.00
q["RADE"]["H3'"] = 0.00
# if O2* atom, C2* could still have 1 Hydrogen
q["RADE"]["H2*"] = 0.00
q["RADE"]["H2'"] = 0.00
q["RADE"]["H1*"] = 0.00
q["RADE"]["H1'"] = 0.00
q["RADE"]["H8"] = 0.00
q["RADE"]["H7"] = 0.00
q["RADE"]["H3"] = 0.00
q["RADE"]["H2"] = 0.00
q["RADE"]["H1"] = 0.00

#  D-THYMINE
q["DTHY"] = q["  T"] = {}
q["DTHY"]["O5*"] = -0.53500
q["DTHY"]["O5'"] = -0.53500
q["DTHY"]["C5*"] = 0.15300
q["DTHY"]["C5'"] = 0.15300
q["DTHY"]["C4*"] = 0.18500
q["DTHY"]["C4'"] = 0.18500
q["DTHY"]["O1*"] = -0.38600
q["DTHY"]["O1'"] = -0.38600
q["DTHY"]["O4*"] = -0.38600
q["DTHY"]["O4'"] = -0.38600
q["DTHY"]["C1*"] = 0.50000
q["DTHY"]["C1'"] = 0.50000
q["DTHY"]["N1"] = -0.73900
q["DTHY"]["C6"] = 0.55100
q["DTHY"]["C5"] = -0.59500
q["DTHY"]["C7"] = 0.09700
q["DTHY"]["C5M"] = 0.09700
q["DTHY"]["C4"] = 0.98000
q["DTHY"]["O4"] = -0.47200
q["DTHY"]["N3"] = -1.01200
q["DTHY"]["H3"] = 0.37000
q["DTHY"]["C2"] = 1.11300
q["DTHY"]["O2"] = -0.52900
q["DTHY"]["C3*"] = 0.17200
q["DTHY"]["C3'"] = 0.17200
q["DTHY"]["C2*"] = -0.04700
q["DTHY"]["C2'"] = -0.04700
q["DTHY"]["O3*"] = -0.53500
q["DTHY"]["O3'"] = -0.53500
q["DTHY"]["P"] = 1.42900
q["DTHY"]["O1P"] = -0.8500
q["DTHY"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["DTHY"]["H1P"] = 0.00
q["DTHY"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["DTHY"]["H5*1"] = 0.00
q["DTHY"]["H5'1"] = 0.00
q["DTHY"]["H5*2"] = 0.00
q["DTHY"]["H5'2"] = 0.00
q["DTHY"]["H4*"] = 0.00
q["DTHY"]["H4'"] = 0.00
q["DTHY"]["H3*"] = 0.00
q["DTHY"]["H3'"] = 0.00
q["DTHY"]["H2*1"] = 0.00
q["DTHY"]["H2'1"] = 0.00
q["DTHY"]["H2*2"] = 0.00
q["DTHY"]["H2'2"] = 0.00
q["DTHY"]["H1*"] = 0.00
q["DTHY"]["H1'"] = 0.00
q["DTHY"]["H6"] = 0.00
q["DTHY"]["H5M1"] = 0.00
q["DTHY"]["H5M2"] = 0.00
q["DTHY"]["H5M3"] = 0.00

#  R-URACIL
q["RURA"] = q["  U"] = {}
q["RURA"]["O5*"] = -0.53500
q["RURA"]["O5'"] = -0.53500
q["RURA"]["C5*"] = 0.17500
q["RURA"]["C5'"] = 0.17500
q["RURA"]["C4*"] = 0.19700
q["RURA"]["C4'"] = 0.19700
q["RURA"]["O1*"] = -0.41300
q["RURA"]["O1'"] = -0.41300
q["RURA"]["O4*"] = -0.41300
q["RURA"]["O4'"] = -0.41300
q["RURA"]["C1*"] = 0.52200
q["RURA"]["C1'"] = 0.52200
q["RURA"]["N1"] = -0.56700
q["RURA"]["C6"] = 0.36600
q["RURA"]["C5"] = -0.20400
q["RURA"]["C4"] = 0.57200
q["RURA"]["O4"] = -0.39400
q["RURA"]["N3"] = -0.75800
q["RURA"]["H3"] = 0.34700
q["RURA"]["C2"] = 0.89600
q["RURA"]["O2"] = -0.49400
q["RURA"]["C3*"] = 0.21000
q["RURA"]["C3'"] = 0.21000
q["RURA"]["C2*"] = 0.08200
q["RURA"]["C2'"] = 0.08200
q["RURA"]["O2*"] = -0.51200
q["RURA"]["O2'"] = -0.51200
q["RURA"]["HO2*"] = 0.31600
q["RURA"]["HO2'"] = 0.31600
q["RURA"]["O3*"] = -0.53500
q["RURA"]["O3'"] = -0.53500
q["RURA"]["P"] = 1.42900
q["RURA"]["O1P"] = -0.8500
q["RURA"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["RURA"]["H1P"] = 0.00
q["RURA"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
# the sugar's nphs
q["RURA"]["H5*1"] = 0.00
q["RURA"]["H5'1"] = 0.00
q["RURA"]["H5*2"] = 0.00
q["RURA"]["H5'2"] = 0.00
q["RURA"]["H4*"] = 0.00
q["RURA"]["H4'"] = 0.00
q["RURA"]["H3*"] = 0.00
q["RURA"]["H3'"] = 0.00
# if O2* atom, C2* could still have 1 Hydrogen
q["RURA"]["H2*"] = 0.00
q["RURA"]["H2'"] = 0.00
q["RURA"]["H1*"] = 0.00
q["RURA"]["H1'"] = 0.00
# the base's nphs
q["RURA"]["H51"] = 0.00
q["RURA"]["H52"] = 0.00
q["RURA"]["H61"] = 0.00
q["RURA"]["H62"] = 0.00

#  D-GUANOSINE
q["DGUA"] = q["  G"] = {}
q["DGUA"]["O5*"] = -0.53500
q["DGUA"]["O5'"] = -0.53500
q["DGUA"]["C5*"] = 0.15300
q["DGUA"]["C5'"] = 0.15300
q["DGUA"]["C4*"] = 0.18500
q["DGUA"]["C4'"] = 0.18500
q["DGUA"]["O1*"] = -0.38600
q["DGUA"]["O1'"] = -0.38600
q["DGUA"]["O4*"] = -0.38600
q["DGUA"]["O4'"] = -0.38600
q["DGUA"]["C1*"] = 0.50000
q["DGUA"]["C1'"] = 0.50000
q["DGUA"]["N9"] = -0.37900
q["DGUA"]["C8"] = 0.42800
q["DGUA"]["N7"] = -0.57500
q["DGUA"]["C5"] = -0.08800
q["DGUA"]["C6"] = 0.71400
q["DGUA"]["O6"] = -0.45900
q["DGUA"]["N1"] = -0.74600
q["DGUA"]["H1"] = 0.34000
q["DGUA"]["C2"] = 0.84200
q["DGUA"]["N2"] = -0.75800
q["DGUA"]["H21"] = 0.32400
q["DGUA"]["H22"] = 0.33300
q["DGUA"]["N3"] = -0.70200
q["DGUA"]["C4"] = 0.49000
q["DGUA"]["C3*"] = 0.17200
q["DGUA"]["C3'"] = 0.17200
q["DGUA"]["C2*"] = -0.04700
q["DGUA"]["C2'"] = -0.04700
q["DGUA"]["O3*"] = -0.53500
q["DGUA"]["O3'"] = -0.53500
q["DGUA"]["P"] = 1.42900
q["DGUA"]["O1P"] = -0.8500
q["DGUA"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["DGUA"]["H1P"] = 0.00
q["DGUA"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["DGUA"]["H5*1"] = 0.00
q["DGUA"]["H5'1"] = 0.00
q["DGUA"]["H5*2"] = 0.00
q["DGUA"]["H5'2"] = 0.00
q["DGUA"]["H4*"] = 0.00
q["DGUA"]["H4'"] = 0.00
q["DGUA"]["H3*"] = 0.00
q["DGUA"]["H3'"] = 0.00
q["DGUA"]["H2*1"] = 0.00
q["DGUA"]["H2'1"] = 0.00
q["DGUA"]["H2*2"] = 0.00
q["DGUA"]["H2'2"] = 0.00
q["DGUA"]["H1*"] = 0.00
q["DGUA"]["H1'"] = 0.00
q["DGUA"]["H8"] = 0.00

#  R-GUANOSINE
q["RGUA"] = q[" RG"] = {}
q["RGUA"]["O5*"] = -0.53500
q["RGUA"]["O5'"] = -0.53500
q["RGUA"]["C5*"] = 0.17500
q["RGUA"]["C5'"] = 0.17500
q["RGUA"]["C4*"] = 0.19700
q["RGUA"]["C4'"] = 0.19700
q["RGUA"]["O1*"] = -0.41300
q["RGUA"]["O1'"] = -0.41300
q["RGUA"]["O4*"] = -0.41300
q["RGUA"]["O4'"] = -0.41300
q["RGUA"]["C1*"] = 0.52200
q["RGUA"]["C1'"] = 0.52200
q["RGUA"]["N9"] = -0.37900
q["RGUA"]["C8"] = 0.42800
q["RGUA"]["N7"] = -0.57500
q["RGUA"]["C5"] = -0.08800
q["RGUA"]["C6"] = 0.71400
q["RGUA"]["O6"] = -0.45900
q["RGUA"]["N1"] = -0.74600
q["RGUA"]["H1"] = 0.34000
q["RGUA"]["C2"] = 0.84200
q["RGUA"]["N2"] = -0.75800
q["RGUA"]["H21"] = 0.32400
q["RGUA"]["H22"] = 0.33300
q["RGUA"]["N3"] = -0.70200
q["RGUA"]["C4"] = 0.49000
q["RGUA"]["C3*"] = 0.21000
q["RGUA"]["C3'"] = 0.21000
q["RGUA"]["C2*"] = 0.08200
q["RGUA"]["C2'"] = 0.08200
q["RGUA"]["O2*"] = -0.51200
q["RGUA"]["O2'"] = -0.51200
q["RGUA"]["HO2*"] = 0.31600
q["RGUA"]["HO2'"] = 0.31600
q["RGUA"]["O3*"] = -0.53500
q["RGUA"]["O3'"] = -0.53500
q["RGUA"]["P"] = 1.42900
q["RGUA"]["O1P"] = -0.8500
q["RGUA"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["RGUA"]["H1P"] = 0.00
q["RGUA"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["RGUA"]["H5*1"] = 0.00
q["RGUA"]["H5'1"] = 0.00
q["RGUA"]["H5*2"] = 0.00
q["RGUA"]["H5'2"] = 0.00
q["RGUA"]["H4*"] = 0.00
q["RGUA"]["H4'"] = 0.00
q["RGUA"]["H3*"] = 0.00
q["RGUA"]["H3'"] = 0.00
# if O2* atom, C2* could still have H2*
q["RGUA"]["H2*"] = 0.00
q["RGUA"]["H2'"] = 0.00
q["RGUA"]["H1*"] = 0.00
q["RGUA"]["H1'"] = 0.00
q["RGUA"]["H8"] = 0.00

#  D-CYTOSINE
q["DCYT"] = q["  C"] = {}
q["DCYT"]["O5*"] = -0.53500
q["DCYT"]["O5'"] = -0.53500
q["DCYT"]["C5*"] = 0.15300
q["DCYT"]["C5'"] = 0.15300
q["DCYT"]["C4*"] = 0.18500
q["DCYT"]["C4'"] = 0.18500
q["DCYT"]["O1*"] = -0.38600
q["DCYT"]["O1'"] = -0.38600
q["DCYT"]["O4*"] = -0.38600
q["DCYT"]["O4'"] = -0.38600
q["DCYT"]["C1*"] = 0.50000
q["DCYT"]["C1'"] = 0.50000
q["DCYT"]["N1"] = -0.57200
q["DCYT"]["C6"] = 0.37700
q["DCYT"]["C5"] = -0.23000
q["DCYT"]["C4"] = 0.63000
q["DCYT"]["N4"] = -0.74300
q["DCYT"]["H41"] = 0.33500
q["DCYT"]["H42"] = 0.33800
q["DCYT"]["N3"] = -0.79100
q["DCYT"]["C2"] = 0.93800
q["DCYT"]["O2"] = -0.51800
q["DCYT"]["C3*"] = 0.17200
q["DCYT"]["C3'"] = 0.17200
q["DCYT"]["C2*"] = -0.04700
q["DCYT"]["C2'"] = -0.04700
q["DCYT"]["O3*"] = -0.53500
q["DCYT"]["O3'"] = -0.53500
q["DCYT"]["P"] = 1.42900
q["DCYT"]["O1P"] = -0.8500
q["DCYT"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["DCYT"]["H1P"] = 0.00
q["DCYT"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["DCYT"]["H5*1"] = 0.00
q["DCYT"]["H5'1"] = 0.00
q["DCYT"]["H5*2"] = 0.00
q["DCYT"]["H5'2"] = 0.00
q["DCYT"]["H4*"] = 0.00
q["DCYT"]["H4'"] = 0.00
q["DCYT"]["H3*"] = 0.00
q["DCYT"]["H3'"] = 0.00
q["DCYT"]["H2*1"] = 0.00
q["DCYT"]["H2'1"] = 0.00
q["DCYT"]["H2*2"] = 0.00
q["DCYT"]["H2'2"] = 0.00
q["DCYT"]["H1*"] = 0.00
q["DCYT"]["H1'"] = 0.00
q["DCYT"]["H5"] = 0.00
q["DCYT"]["H6"] = 0.00

#   R-CYTOSINE
q["RCYT"] = q[" RC"] = {}
q["RCYT"]["O5*"] = -0.53500
q["RCYT"]["O5'"] = -0.53500
q["RCYT"]["C5*"] = 0.17500
q["RCYT"]["C5'"] = 0.17500
q["RCYT"]["C4*"] = 0.19700
q["RCYT"]["C4'"] = 0.19700
q["RCYT"]["O1*"] = -0.41300
q["RCYT"]["O1'"] = -0.41300
q["RCYT"]["O4*"] = -0.41300
q["RCYT"]["O4'"] = -0.41300
q["RCYT"]["C1*"] = 0.52200
q["RCYT"]["C1'"] = 0.52200
q["RCYT"]["N1"] = -0.57200
q["RCYT"]["C6"] = 0.37700
q["RCYT"]["C5"] = -0.23000
q["RCYT"]["C4"] = 0.63000
q["RCYT"]["N4"] = -0.74300
q["RCYT"]["H41"] = 0.33500
q["RCYT"]["H42"] = 0.33800
q["RCYT"]["N3"] = -0.79100
q["RCYT"]["C2"] = 0.93800
q["RCYT"]["O2"] = -0.51800
q["RCYT"]["C3*"] = 0.21000
q["RCYT"]["C3'"] = 0.21000
q["RCYT"]["C2*"] = 0.08200
q["RCYT"]["C2'"] = 0.08200
q["RCYT"]["O2*"] = -0.51200
q["RCYT"]["O2'"] = -0.51200
q["RCYT"]["HO2*"] = 0.31600
q["RCYT"]["HO2'"] = 0.31600
q["RCYT"]["O3*"] = -0.53500
q["RCYT"]["O3'"] = -0.53500
q["RCYT"]["P"] = 1.42900
q["RCYT"]["O1P"] = -0.8500
q["RCYT"]["O2P"] = -0.8500
# no charges available for these hydrogens:
q["RCYT"]["H1P"] = 0.00
q["RCYT"]["H2P"] = 0.00
# possible other nph names generated by add_hydrogens
q["RCYT"]["H5*1"] = 0.00
q["RCYT"]["H5'1"] = 0.00
q["RCYT"]["H5*2"] = 0.00
q["RCYT"]["H5'2"] = 0.00
q["RCYT"]["H4*"] = 0.00
q["RCYT"]["H4'"] = 0.00
q["RCYT"]["H3*"] = 0.00
q["RCYT"]["H3'"] = 0.00
# if O2* atom, C2* could still have 1 Hydrogen
q["RCYT"]["H2*"] = 0.00
q["RCYT"]["H2'"] = 0.00
q["RCYT"]["H1*"] = 0.00
q["RCYT"]["H1'"] = 0.00
q["RCYT"]["H5"] = 0.00
q["RCYT"]["H6"] = 0.00

#  D - PHOSPATE MINUS
q["DPOM"] = {}
q["DPOM"]["P"] = 1.42900
q["DPOM"]["OA"] = -0.85000
q["DPOM"]["OB"] = -0.85000
# possible other nph names generated by add_hydrogens
q["DPOM"]["HOA"] = 0.00
q["DPOM"]["HOB"] = 0.00
q["DPOM"]["HOL"] = 0.00
q["DPOM"]["HOR"] = 0.00

#  R - PHOSPHATE MINUS
q["RPOM"] = {}
q["RPOM"]["P"] = 1.42900
q["RPOM"]["OA"] = -0.85000
q["RPOM"]["OB"] = -0.85000
# possible other nph names generated by add_hydrogens
q["RPOM"]["HOA"] = 0.00
q["RPOM"]["HOB"] = 0.00
q["RPOM"]["HOL"] = 0.00
q["RPOM"]["HOR"] = 0.00
